/*
 * DNA.h
 *
 *  Created on: Apr 19, 2011
 *      Author: James Harding
 */

#ifndef DNA_H_
#define DNA_H_

class DNA{
	public:
		DNA();
		DNA(int originalSize);
		DNA(std::vector<char> newDNASequence);
		~DNA();

		void printDNASequenceOriginal();
		void printDNASequenceAligned();
		void clearAligned();

		bool AddToDNASequenceOriginal(char residue);
		bool AddToDNASequenceAligned(char residue);

		bool InsertAtBeginingAligned(char residue);

		char getDNAatPositionOriginal(int position);
		char getDNAatPositionAligned(int position);

		int getOriginalSize();
		int getAlignedSize();

	private:
		//Global variables of the class
		std::vector<char> DNASequenceOriginal;
		std::vector<char> DNASequenceAligned;
		int DNAAlignedPosition;
		int DNAOriginalPosition;
};



#endif /* DNA_H_ */
